pyfaidx

pyfaidx retrieves subsequences from FASTA files using on-disk indexing to enable memory-efficient access and manipulation of genomic sequences.

Key Features:

• On-disk FASTA indexing: Provides an index of FASTA files that enables random access to sequences without loading entire files into memory.
• Memory-efficient subsequence retrieval: Allows extraction of subsequences directly from disk to support large genomic datasets.
• Dictionary-like sequence access: Exposes Python classes that map FASTA headers to sequences and support positional slicing.
• samtools index compatibility: Produces and uses index files compatible with samtools indexing formats.
• In-place FASTA modification: Supports modifications to FASTA files while leveraging the on-disk index.
• Test suite for reproducibility: Includes automated tests to verify correct and reproducible behavior.

Scientific Applications:

• Large-scale genomic data handling: Enables access to specific regions of large FASTA files without full-file reads, facilitating analyses on large genomes.
• Integration with alignment workflows: Provides samtools-compatible indexing to support sequence retrieval for sequence alignment and downstream analysis workflows.
• Targeted subsequence extraction: Supports positional slicing for extracting regions of interest for downstream computational analyses.

Methodology:

Builds on on-disk FASTA indexing (samtools-compatible), dictionary-like Python classes that map headers to sequences, positional slicing to retrieve subsequences without loading entire files, and support for in-place FASTA modification.